public class SmilesBond extends Edge
Modifier and Type | Field and Description |
---|---|
(package private) SmilesAtom |
atom1 |
(package private) SmilesAtom |
atom2 |
(package private) SmilesBond[] |
bondsOr |
(package private) boolean |
isNot |
(package private) boolean |
isRingBond |
(package private) Edge |
matchingBond |
(package private) int |
nBondsOr |
(package private) int |
nPrimitives |
(package private) SmilesBond[] |
primitives |
static int |
TYPE_ANY |
static int |
TYPE_AROMATIC |
static int |
TYPE_ATROPISOMER_1 |
static int |
TYPE_ATROPISOMER_2 |
static int |
TYPE_BIO_CROSSLINK |
static int |
TYPE_BIO_SEQUENCE |
static int |
TYPE_DIRECTIONAL_1 |
static int |
TYPE_DIRECTIONAL_2 |
static int |
TYPE_DOUBLE |
static int |
TYPE_MULTIPLE |
static int |
TYPE_NONE |
static int |
TYPE_RING |
static int |
TYPE_SINGLE |
static int |
TYPE_TRIPLE |
static int |
TYPE_UNKNOWN |
argbsHbondType, BOND_AROMATIC, BOND_AROMATIC_DOUBLE, BOND_AROMATIC_MASK, BOND_AROMATIC_SINGLE, BOND_COVALENT_DOUBLE, BOND_COVALENT_MASK, BOND_COVALENT_QUADRUPLE, BOND_COVALENT_SINGLE, BOND_COVALENT_TRIPLE, BOND_H_CALC, BOND_H_CALC_MASK, BOND_H_MINUS_3, BOND_H_MINUS_4, BOND_H_NUCLEOTIDE, BOND_H_PLUS_2, BOND_H_PLUS_3, BOND_H_PLUS_4, BOND_H_PLUS_5, BOND_H_REGULAR, BOND_HBOND_SHIFT, BOND_HYDROGEN_MASK, BOND_NEW, BOND_ORDER_ANY, BOND_ORDER_NULL, BOND_ORDER_UNSPECIFIED, BOND_PARTIAL_MASK, BOND_PARTIAL01, BOND_PARTIAL12, BOND_PARTIAL23, BOND_PARTIAL32, BOND_PYMOL_MULT, BOND_PYMOL_SINGLE, BOND_STEREO_FAR, BOND_STEREO_MASK, BOND_STEREO_NEAR, BOND_STRUT, BOND_SULFUR_MASK, FLAG_AROMATIC_DEFINED, FLAG_AROMATIC_DOUBLE, FLAG_AROMATIC_NONCANONICAL, FLAG_AROMATIC_STRICT, FLAG_IGNORE_STEREOCHEMISTRY, FLAG_INVERT_STEREOCHEMISTRY, FLAG_NO_AROMATIC, index, order
Constructor and Description |
---|
SmilesBond(SmilesAtom atom1,
SmilesAtom atom2,
int bondType,
boolean isNot)
SmilesBond constructor
|
Modifier and Type | Method and Description |
---|---|
(package private) SmilesBond |
addBondOr() |
(package private) SmilesBond |
addPrimitive() |
int |
getAtomIndex1() |
int |
getAtomIndex2() |
(package private) static java.lang.String |
getBondOrderString(int order) |
(package private) int |
getBondType() |
(package private) static int |
getBondTypeFromCode(char code) |
int |
getCovalentOrder() |
(package private) SmilesAtom |
getOtherAtom(SmilesAtom a) |
Node |
getOtherAtomNode(Node atom) |
(package private) int |
getValence() |
(package private) static boolean |
isBondType(char ch,
boolean isSearch,
boolean isBioSequence) |
boolean |
isCovalent() |
boolean |
isHydrogen() |
(package private) void |
set(SmilesBond bond) |
(package private) void |
set2(int bondType,
boolean isNot) |
(package private) void |
set2a(SmilesAtom atom1,
SmilesAtom atom2) |
(package private) void |
setAtom2(SmilesAtom atom)
from parse ring
|
(package private) void |
switchAtoms() |
java.lang.String |
toString() |
getArgbHbondType, getBondOrderFromFloat, getBondOrderFromString, getBondOrderNameFromOrder, getBondOrderNumberFromOrder, getCmlBondOrder, getCovalentBondOrder, getPartialBondDotted, getPartialBondOrder
public static final int TYPE_UNKNOWN
public static final int TYPE_NONE
public static final int TYPE_SINGLE
public static final int TYPE_DOUBLE
public static final int TYPE_TRIPLE
public static final int TYPE_AROMATIC
public static final int TYPE_DIRECTIONAL_1
public static final int TYPE_DIRECTIONAL_2
public static final int TYPE_ATROPISOMER_1
public static final int TYPE_ATROPISOMER_2
public static final int TYPE_RING
public static final int TYPE_ANY
public static final int TYPE_BIO_SEQUENCE
public static final int TYPE_BIO_CROSSLINK
public static final int TYPE_MULTIPLE
SmilesAtom atom1
SmilesAtom atom2
boolean isNot
Edge matchingBond
SmilesBond[] primitives
int nPrimitives
SmilesBond[] bondsOr
int nBondsOr
boolean isRingBond
SmilesBond(SmilesAtom atom1, SmilesAtom atom2, int bondType, boolean isNot)
atom1
- First atomatom2
- Second atombondType
- Bond typeisNot
- static java.lang.String getBondOrderString(int order)
void set(SmilesBond bond)
SmilesBond addBondOr()
SmilesBond addPrimitive()
public java.lang.String toString()
toString
in class java.lang.Object
void set2(int bondType, boolean isNot)
void set2a(SmilesAtom atom1, SmilesAtom atom2)
void setAtom2(SmilesAtom atom)
atom
- static boolean isBondType(char ch, boolean isSearch, boolean isBioSequence) throws InvalidSmilesException
InvalidSmilesException
static int getBondTypeFromCode(char code)
code
- Bond codeint getBondType()
int getValence()
SmilesAtom getOtherAtom(SmilesAtom a)
public int getAtomIndex1()
getAtomIndex1
in class Edge
public int getAtomIndex2()
getAtomIndex2
in class Edge
public int getCovalentOrder()
getCovalentOrder
in class Edge
public Node getOtherAtomNode(Node atom)
getOtherAtomNode
in class Edge
public boolean isCovalent()
isCovalent
in class Edge
public boolean isHydrogen()
isHydrogen
in class Edge
void switchAtoms()